metadata

license: apache-2.0
task_categories:
  - text-classification
language:
  - en
tags:
  - LucaOne
  - Bioinformatics
  - Protein
  - Gene
  - RNA
  - DNA
  - Nucleic Acid
  - Interaction
  - AI4Biology
  - Bio
  - Biology
  - AI4Science
pretty_name: LucaGroup/LucaOne-Downstream-Task-Datasets

split: dev
path: dataset/ncRNAFam/gene/multi_class/dev/dev.csv
split: test
path: dataset/ncRNAFam/gene/multi_class/test/test.csv
split: label
path: dataset/ncRNAFam/gene/multi_class/label.txt
config_name: ncRPI
data_files:
- split: train
  path: dataset/ncRPI/gene_protein/binary_class/train/train.csv
- split: dev
  path: dataset/ncRPI/gene_protein/binary_class/dev/dev.csv
- split: test
  path: dataset/ncRPI/gene_protein/binary_class/test/test.csv
config_name: PPI
data_files:
- split: train
  path: dataset/PPI/protein/binary_class/train/train.csv
- split: dev
  path: dataset/PPI/protein/binary_class/dev/dev.csv
- split: test
  path: dataset/PPI/protein/binary_class/test/test.csv
config_name: ProtLoc
data_files:
- split: train
  path: dataset/ProtLoc/protein/multi_class/train/train.csv
- split: dev
  path: dataset/ProtLoc/protein/multi_class/dev/dev.csv
- split: test
  path: dataset/ProtLoc/protein/multi_class/test/test.csv
config_name: ProtLocCDSGene
data_files:
- split: train
  path: dataset/ProtLocCDSGene/gene/multi_class/train/train.csv
- split: dev
  path: dataset/ProtLocCDSGene/gene/multi_class/dev/dev.csv
- split: test
  path: dataset/ProtLocCDSGene/gene/multi_class/test/test.csv
config_name: ProtLocCDSProt
data_files:
- split: train
  path: dataset/ProtLocCDSProt/protein/multi_class/train/train.csv
- split: dev
  path: dataset/ProtLocCDSProt/protein/multi_class/dev/dev.csv
- split: test
  path: dataset/ProtLocCDSProt/protein/multi_class/test/test.csv
- split: label
  path: dataset/ProtLocCDSProt/protein/multi_class/label.txt
config_name: ProtStab
data_files:
- split: train
  path: dataset/ProtStab/protein/regression/train/train.csv
- split: dev
  path: dataset/ProtStab/protein/regression/dev/dev.csv
- split: test
  path: dataset/ProtStab/protein/regression/test/test.csv
config_name: SpeciesTax
data_files:
- split: train
  path: dataset/SpeciesTax/gene/multi_class/train/train.csv
- split: dev
  path: dataset/SpeciesTax/gene/multi_class/dev/dev.csv
- split: test
  path: dataset/SpeciesTax/gene/multi_class/test/test.csv
config_name: SupKTax
data_files:
- split: train
  path: dataset/SupKTax/gene/multi_class/train/train.csv
- split: dev
  path: dataset/SupKTax/gene/multi_class/dev/dev.csv
- split: test
  path: dataset/SupKTax/gene/multi_class/test/test.csv

LucaOne-Downstream-Task-Datasets

This directory includes all the downstream task datasets of the LucaOne paper (https://www.nature.com/articles/s42256-025-01044-4).

Dataset Structure

This dataset includes three splits and a label info file:

train(training dataset)
dev (validation dataset)
test (testing dataset)
label.txt (label name to label index in *.csv, label_idx=${the line number of label_name - 1})

Usage:

from datasets import load_dataset


# load ncRPI dataset
ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI")

Github

https://github.com/LucaOne/ - split: dev
path: dataset/ncRNAFam/gene/multi_class/dev/dev.csv

split: test
path: dataset/ncRNAFam/gene/multi_class/test/test.csv
split: label
path: dataset/ncRNAFam/gene/multi_class/label.txt
config_name: ncRPI
data_files:
- split: train
  path: dataset/ncRPI/gene_protein/binary_class/train/train.csv
- split: dev
  path: dataset/ncRPI/gene_protein/binary_class/dev/dev.csv
- split: test
  path: dataset/ncRPI/gene_protein/binary_class/test/test.csv
config_name: PPI
data_files:
- split: train
  path: dataset/PPI/protein/binary_class/train/train.csv
- split: dev
  path: dataset/PPI/protein/binary_class/dev/dev.csv
- split: test
  path: dataset/PPI/protein/binary_class/test/test.csv
config_name: ProtLoc
data_files:
- split: train
  path: dataset/ProtLoc/protein/multi_class/train/train.csv
- split: dev
  path: dataset/ProtLoc/protein/multi_class/dev/dev.csv
- split: test
  path: dataset/ProtLoc/protein/multi_class/test/test.csv
config_name: ProtLocCDSGene
data_files:
- split: train
  path: dataset/ProtLocCDSGene/gene/multi_class/train/train.csv
- split: dev
  path: dataset/ProtLocCDSGene/gene/multi_class/dev/dev.csv
- split: test
  path: dataset/ProtLocCDSGene/gene/multi_class/test/test.csv
config_name: ProtLocCDSProt
data_files:
- split: train
  path: dataset/ProtLocCDSProt/protein/multi_class/train/train.csv
- split: dev
  path: dataset/ProtLocCDSProt/protein/multi_class/dev/dev.csv
- split: test
  path: dataset/ProtLocCDSProt/protein/multi_class/test/test.csv
- split: label
  path: dataset/ProtLocCDSProt/protein/multi_class/label.txt
config_name: ProtStab
data_files:
- split: train
  path: dataset/ProtStab/protein/regression/train/train.csv
- split: dev
  path: dataset/ProtStab/protein/regression/dev/dev.csv
- split: test
  path: dataset/ProtStab/protein/regression/test/test.csv
config_name: SpeciesTax
data_files:
- split: train
  path: dataset/SpeciesTax/gene/multi_class/train/train.csv
- split: dev
  path: dataset/SpeciesTax/gene/multi_class/dev/dev.csv
- split: test
  path: dataset/SpeciesTax/gene/multi_class/test/test.csv
config_name: SupKTax
data_files:
- split: train
  path: dataset/SupKTax/gene/multi_class/train/train.csv
- split: dev
  path: dataset/SupKTax/gene/multi_class/dev/dev.csv
- split: test
  path: dataset/SupKTax/gene/multi_class/test/test.csv